[English] 日本語
Yorodumi
- PDB-6uqd: Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uqd
TitleCo-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small molecule inhibitor
ComponentsStreptopain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / speb / streptopain / inhibitor / nitrile / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


: / streptopain / symbiont-induced defense-related programmed cell death / symbiont-mediated suppression of host autophagy / symbiont-mediated evasion of host immune response / host cell cytosol / cysteine-type peptidase activity / toxin activity / host extracellular space / cysteine-type endopeptidase activity ...: / streptopain / symbiont-induced defense-related programmed cell death / symbiont-mediated suppression of host autophagy / symbiont-mediated evasion of host immune response / host cell cytosol / cysteine-type peptidase activity / toxin activity / host extracellular space / cysteine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10, streptopain superfmaily / Peptidase C10 family / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-QF4 / Streptopain
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsWolan, D.W. / Woehl, J.L. / Kitamura, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Sulfur(VI) Fluoride Exchange (SuFEx)-Enabled High-Throughput Medicinal Chemistry.
Authors: Kitamura, S. / Zheng, Q. / Woehl, J.L. / Solania, A. / Chen, E. / Dillon, N. / Hull, M.V. / Kotaniguchi, M. / Cappiello, J.R. / Kitamura, S. / Nizet, V. / Sharpless, K.B. / Wolan, D.W.
History
DepositionOct 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptopain
B: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0794
Polymers83,1042
Non-polymers9752
Water6,936385
1
A: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0392
Polymers41,5521
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0392
Polymers41,5521
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.624, 115.516, 50.265
Angle α, β, γ (deg.)90.000, 112.580, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Streptopain / Exotoxin type B / SPE B / Streptococcal cysteine proteinase / Streptococcus peptidase A / SPP


Mass: 41551.945 Da / Num. of mol.: 2 / Fragment: UNP residues 28-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: speB / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0J0, streptopain
#2: Chemical ChemComp-QF4 / benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl)(fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate


Mass: 487.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26FN5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.47 Å3/Da / Density % sol: 16.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1-0.15 M sodium nitrate, 22-27% PEG3350 / PH range: 6.8-7.3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.02→43.07 Å / Num. obs: 29212 / % possible obs: 94.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 7.2
Reflection shellResolution: 2.02→2.05 Å / Rmerge(I) obs: 0.544 / Num. unique obs: 1464 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RKX

4rkx


Resolution: 2.02→43.07 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.257 1384 4.74 %
Rwork0.215 27797 -
obs0.217 29181 93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.63 Å2 / Biso mean: 14.77 Å2 / Biso min: 2.33 Å2
Refinement stepCycle: final / Resolution: 2.02→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 68 385 4306
Biso mean--32.08 23.84 -
Num. residues----501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0224-2.09470.34091070.27252364247178
2.0947-2.17860.29181470.25192709285692
2.1786-2.27770.27411600.2362824298495
2.2777-2.39780.28161420.22552877301997
2.3978-2.5480.28991410.22522897303897
2.548-2.74470.27141360.22252832296895
2.7447-3.02090.31941030.22282806290993
3.0209-3.45790.24461480.19882897304597
3.4579-4.35590.20031560.17892765292193
4.3559-43.0660.22051440.19562826297093
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22730.08560.80080.41870.11620.53070.02960.3792-0.0225-0.09560.0058-0.12240.10040.14330.16530.1070.02820.00870.1041-0.01330.08644.6073-23.441415.4609
20.5983-0.0271-0.01810.8123-0.19880.70510.0345-0.1743-0.04620.0007-0.03690.1678-0.0298-0.0069-0.03180.0448-0.0136-0.00760.04270.01040.0548-10.6729-14.14931.8187
30.8808-0.3389-0.25450.1940.03140.68770.0430.0561-0.02690.0083-0.141-0.08370.09140.02850.00010.08-0.0019-0.00790.08080.01660.07020.8908-20.799933.5167
40.1248-0.09540.0160.20330.07611.1863-0.06820.05590.0803-0.0740.04310.0115-0.2137-0.04710.32780.063-0.0026-0.03060.0510.01140.0681-4.4909-5.91920.3618
50.1786-0.15890.12240.79990.18640.9508-0.0150.04430.1174-0.1039-0.0587-0.0983-0.06970.092-0.03060.07490.00240.0230.08370.00760.0664-0.1914-11.55138.6762
61.9044-0.38780.40810.6485-0.10990.567-0.01820.1777-0.06890.0434-0.04750.0310.29410.0815-0.1790.12790.0145-0.02080.0157-0.00270.033-4.3942-20.95749.2379
71.87730.53110.32690.99920.17611.6828-0.065-0.0277-0.1895-0.01880.006-0.15090.1793-0.2184-0.84450.12430.0442-0.01180.0285-0.00050.0497-7.4141-14.096112.0481
81.24940.2499-0.29311.21340.18880.99150.04870.08080.0297-0.09190.01130.0961-0.16370.01410.06490.0620.019-0.02580.03460.00720.03844.89618.21250.1412
90.6112-0.1985-0.00350.5847-0.20170.5583-0.04360.1119-0.0994-0.07330.0387-0.00230.23410.10510.0990.1119-0.02490.00990.114-0.04440.0444.00818.5136-13.0913
100.8575-0.22190.07820.86580.27280.51190.08980.16860.1030.0307-0.0478-0.3548-0.00660.09810.42070.03570.0133-0.00280.0745-0.00170.090716.159323.47092.5833
110.65070.58560.09441.20140.01330.1454-0.1520.1774-0.035-0.10550.1395-0.2355-0.02220.03140.01230.0552-0.0015-0.00020.06130.00080.1112.017818.3278-2.7333
120.52940.0116-0.32880.54370.15890.8531-0.0806-0.0696-0.16340.0011-0.05320.00530.2137-0.0974-0.89020.0888-0.0440.0080.07260.05090.04921.59826.15775.9651
131.4218-0.282-0.0660.8276-0.2110.85630.1754-0.17520.04650.10230.11820.24360.0017-0.24871.42480.0875-0.01920.03710.11090.06880.0942-4.672310.740722.2823
142.56990.10011.46790.75570.28331.7953-0.0663-0.1721-0.0101-0.1210.0363-0.0223-0.2546-0.0986-0.04140.05250.0280.0127-0.03680.02160.0411-3.836715.330510.6632
150.50480.246-0.19070.92170.05830.60280.0581-0.03410.05930.0924-0.02420.1941-0.007-0.0781-0.02390.031-0.00970.01030.0612-0.01440.1127-7.63919.105511.9082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 146 THROUGH 161 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 162 THROUGH 237 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 238 THROUGH 272 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 273 THROUGH 311 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 312 THROUGH 337 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 338 THROUGH 372 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 373 THROUGH 398 )A0
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 146 THROUGH 217 )B0
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 218 THROUGH 237 )B0
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 238 THROUGH 254 )B0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 255 THROUGH 272 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 273 THROUGH 311 )B0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 312 THROUGH 324 )B0
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 325 THROUGH 347 )B0
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 348 THROUGH 399 )B0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more